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massSight

DOI

massSight is an R package for the alignment and scaling of LC-MS metabolomics data.

Contents

Examples

Examples and extensive documentation can be found here

Installation 

devtools::install_github("omicsEye/massSight")

Data Preparation

massSight works with the output of LC-MS experiments, which should contain columns corresponding to:

  1. Compound ID
  2. Retention Time
  3. Mass to Charge Ratio
  4. (Optional) Average Intensity across all samples
  5. (Optional) Metabolite Name
Compound_ID MZ RT Intensity Metabolite
CMP-2758 197.0665 3.401200 74498.87 1,7-dimethyluric acid
CMP-4802 282.1189 8.627617 25684.75 1-methyladenosine
CMP-3329 166.0720 6.069083 28585.37 1-methylguanine
CMP-3294 298.1139 5.913067 61491.94 1-methylguanosine
CMP-5077 137.0707 9.114433 112107.07 1-methylnicotinamide
CMP-1830 347.2210 2.017650 1291.29 21-deoxycortisol

The massSight Object

massSight creates and uses the MSObject class to store data and results pertaining to individual LC-MS experiments. Prior to alignment, LC-MS data frames or tibbles should be converted into an MSObject using create_ms_obj:

ms1 <-
  create_ms_obj(
    df = hp1,
    name = "hp1",
    id_name = "Compound_ID",
    rt_name = "RT",
    mz_name = "MZ",
    int_name = "Intensity"
  )

ms2 <-
  create_ms_obj(
    df = hp2,
    name = "hp2",
    id_name = "Compound_ID",
    rt_name = "RT",
    mz_name = "MZ",
    int_name = "Intensity"
  )

An MSObject provides the following functions:

  • raw_df() to access the experiment’s raw LC-MS data
  • isolated() to access the experiment’s isolated metabolites, which is important for downstream alignment tasks
  • scaled_df() to access the experiment’s scaled LC-MS data
  • consolidated() to access the experiment’s consolidated data
  • metadata() to access the experiment’s metadata
ms2 |>
  raw_df() |>
  head() |>
  kableExtra::kbl(format = "simple")
Compound_ID RT MZ Intensity
1.68_121.1013m/z 1.68 121.1013 50543.745
3.53_197.0667m/z 3.53 197.0667 21948.556
7.81_282.1190m/z 7.81 282.1190 14220.869
5.29_166.0721m/z 5.29 166.0721 46434.807
5.16_298.1139m/z 5.16 298.1139 60616.582
9.77_126.1026m/z 9.77 126.1026 4435.973

Alignment

Alignment is performed using auto_combine()

aligned <- auto_combine(ms1 = ms1, 
                      ms2 = ms2, 
                      iso_method = "dbscan")

More information on the auto_combine() function can be found in the package documentation

Plotting results from alignment 

final_plots(aligned)

Citation

If you use our package, please cite us via our Zenodo upload

Additional citation formats can be found via the Zenodo link.

Dev Instructions

Installation

  1. Clone/pull massSight
  2. Open the R project massSight.Rproj
  3. Build package using devtools::build()
  4. Install package using devtools::install()